I am hospitalized w/ pnemonia and possibly whooping cough. Blood test came back pos for staph. How serious is staph infection in the lungs?

Very. If you have positive blood cultures for staph aureus (ask your doctor what species of staph since if it is coagulase negative it is probably a contaminant) you are very seriously ill and infective endocarditis must be excluded from your diagnosis. You need to be seen in consultation by an infectious diseases expert. Hope you get over this soon. Good luck.

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Can the morning after pill appear in a blood test for whooping cough?

No. I trust you are referring to a blood test to see if a person has immunity to whooping cough. Such tests are not designed to detect use of birth control pills, including morning after pill. Read more...